Background: Integrated Management of Childhood Illness (IMCI) is an effective 11-day standard training; however, due to budgetary expenses and human resource constraints, many health professionals cannot take 11 days off work. As a result, shortened training curriculums (6-day) have been proposed. We used a cross-sectional study to evaluate the effect of this shortened training on appropriate IMCI classification and treatment of under-five childhood illness management in Rwanda. Methods: A cross-sectional study was conducted in 22 health centers in Rwanda, comparing data from 121 nurses, where 55 nurses completed the 11-day and 66 nurses completed the 6-day training. Among 768 children, we evaluated clinical outcomes from May 2011 to April 2012. Descriptive statistics were used to display the sociodemographic characteristics of health providers; including level of education, sex, age, and professional experiences. Bivariable and multivariable analyses were used to test for differences between nurses in the 6-day versus 11-day training on the appropriate classification and treatment of childhood illness. Results: Our findings show that at the bivariable level and after controlling for confounders in the multivariable analysis, the only significant differences detected between nurses in the long and short training was the classification of fever (adjusted odds ratio [aOR] 0.7, 95% confidence interval [CI] 0.64–0.75) and treatment of pneumonia (aOR 0.8, 95% CI 0.70–0.89). Nurses in the short training had lower odds of inappropriate misclassification and treatment for these two conditions. Conclusion: There was no difference in classification and treatment of childhood illness among nurses who completed the standard and short IMCI training courses. Short-training could be a more cost-saving option for health facilities without compromising the key outcomes related to case management.